Deny directory indexes doesn't work

I'm managing my server using ISPConfig. All the sites set up in ISPConfig have no problems denying directory content. If I create a new directory via ftp I will get a 403 Forbidden trying to access it.

However the default Apache site /var/www, answering on my servers IP adress on a http request, shows all directory content except for some directories like /clients. If I create a new directory via ftp it will be open for directory listing.

I've been setting Options -Indexes in .htaccess files and httpd.conf and indexes are still open.

In the debian, with default installation with no changes in both files, you can use it... if you have another distro or this is not your scenario, just edit manually (add "-" in Options Indexes for Directory /var/www/)